Flores was designated for assignment by the Marlins on Tuesday.
The Marlins activated Justin Bour off the 60-day disabled list Tuesday, so a 40-man roster spot needed to be cleared in order to get the hard-hitting first baseman back to Miami. Flores ended up being the odd man out despite pushing for a spot in the big league bullpen before early-season shoulder issues derailed his season. The 24-year-old put together good campaigns in the minor leagues in the past, so there's a good chance that he'll end up back on the 40-man roster prior to the start of next season, but for the time being he'll have to wait for another crack at the major leagues.